In the Sonoran desert, there exists a diverse community of cactophilic drosophilids that exploit toxic, rotting cactus tissue as a food resource. The chemistry of the necrotic cactus tissue varies among species, and several drosphilid species have evolved specialized detoxification mechanisms and a preference for certain cactus types. In the present study, we compared the genetic structure of two columnar cactus species, Drosophila mettleri and Drosophila mojavensis, and two prickly pear species, Drosophila mainlandi and Drosophila hamatofila, which have all recently colonized Catalina Island off the coast of southern California. Because there are no columnar cactus species on Catalina Island, the two columnar specialists underwent a host switch to prickly pear cactus, the only cactus present on the island. Previous genetic studies of D. mettleri and D. mojavensis showed significant genetic differentiation between mainland and island populations, which could result from restricted gene flow as a result of the San Pedro Channel, or because of a host switch to prickly pear. To distinguish between these possibilities, we analyzed the genetic structure of the prickly pear species aiming to isolate the effects of geography versus host switching. The results obtained show little to no genetic differentiation for the prickly pear species, supporting the hypothesis that the genetic differentiation of the two columnar species is a result of a host switch from columnar cacti to prickly pear. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.